Intra-leaf gradients of photoinhibition induced by different color lights: implications for the dual mechanisms of photoinhibition and for the application of conventional chlorophyll fluorometers

? We studied how different color lights cause gradients of photoinhibition within a leaf, to attempt to resolve the controversy of whether photon absorption by chlorophyll or by manganese (Mn) is the primary cause of photoinhibition, as suggested by the excess-energy hypothesis or the two-step hypothesis, respectively. ? Lincomycin-treated leaf discs were photoinhibited by white, blue, green or red light. Combining a microfiber fluorometer, a fiber-thinning technique and a micro-manipulator enabled us to measure the chlorophyll fluorescence signals within a leaf. Photoinhibition gradients were also compared with results from various conventional fluorometers to estimate their depth of signal detection. ? The severity of photoinhibition was in the descending order of blue, red and green light near the adaxial surface, and in the descending order of blue, green and red light in the deeper tissue, which correlated with the chlorophyll and the Mn absorption spectrums, respectively. These results cannot be explained by either hypothesis alone. ? These data strongly suggest that both the excess-energy and the two-step mechanisms occur in photoinhibition, and fluorometers with red or blue measuring light give overestimated or underestimated F(v)/F(m) values of photoinhibited leaves compared with the whole tissue average, respectively; that is, they measured deeper or shallower leaf tissue, respectively.     

Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium

The complete genome sequencing of a γ-hexachlorocyclohexane-degrading strain, Sphingobium japonicum UT26, revealed that the genome consists of two circular chromosomes [with sizes of 3.5 Mb (Chr1) and 682kb (Chr2)], a 191-kb large plasmid (pCHQ1), and two small plasmids with sizes of 32 and 5kb. The lin genes are dispersed on Chr1, Chr2, and pCHQ1. Comparison of the UT26 genome with those of other sphingomonad strains demonstrated that the "specific"lin genes for conversion of γ-HCH to β-ketoadipate (linA, linB, linC, linRED, and linF) are located on the DNA regions unique to the UT26 genome, suggesting the acquisition of these lin genes by horizontal transfer events. On the other hand, linGHIJ and linKLMN are located on the regions conserved in the genomes of sphingomonads, suggesting that the linGHIJ-encoded β-ketoadipate pathway and the LinKLMN-type ABC transporter system are involved in core functions of sphingomonads. Based on these results, we propose a hypothesis that UT26 was created by recruiting the specific lin genes into a strain having core functions of sphingomonads. Most of the specific lin genes in UT26 are associated with IS6100. Our analysis of spontaneous linA-, linC-, and linRED-deletion mutants of UT26 revealed the involvement of IS6100 in their deduced genome rearrangements. These facts strongly suggest that IS6100 plays important roles both in the dissemination of the specific lin genes and in the genome rearrangements.     

Gene analysis and dynamics of tumor stem cells in human glioblastoma cells after radiation

Glioblastoma is the most malignant central nervous system tumor. Patients with glioblastoma are treated with a combination of surgery, radiotherapy and chemotherapy; however, this effect is not satisfactory with regard to the prognosis. It is reported that the tumor stem cells affect recurrence, and radio- and chemotherapy resistance of the tumor, and that these cells play an important role in tumorigenesis and tumor progression. Using human glioblastoma cell lines (T98G and A172), irradiated (0, 30, 60 Gy) glioblastoma cells were prepared under the same conditions as clinical therapy. We analyzed cell proliferation rate, side population analysis by fluorescence-activated cell sorting and isolation of CD133⁺ cells, and performed genetic analysis (human stem cells) on these cells. We also investigated the difference in gene expression in the cells after radiation. The stem cell-related genes were highly expressed in the CD133⁺ cells compared with the CD133^? cells, suggesting that the cancer stem cells may be located in these CD133⁺ cells. In the T98G cell line, the cell proliferation rate of 30-Gy irradiated cells was higher than those of non-irradiated cells and 60-Gy irradiated cells. Stem cell-related genes were highly expressed in 30-Gy irradiated CD133⁺ T98G cells. In conclusion, we suggest that CD133⁺ cells may strongly affect tumor proliferation and the resistance against radiation therapy.     

Ontogenetic patterns of constitutive immune parameters in altricial house sparrows

Innate immune functions are proposed to develop rapidly post‐hatch in altricial nestlings, compared with adaptive immune defenses that require development of receptor specificity and memory. Studies of ontogenetic changes in altricial birds have been few until relatively recently and often do not encompass the entire developmental period. We examined the patterns of development in constitutive innate and adaptive immune indices in house sparrow nestlings (3, 6, 9 and 12 days (d) post‐hatch), hatch‐year birds and adults. Lysozyme activity significantly decreased with age, likely representing catabolism of maternal investment of lysozyme in the egg albumen. Levels of total IgY (indexing adaptive immune function), as well as agglutination and lysis (indexing innate immune function), increased throughout the nestling period, but were significantly below levels found in fully‐grown birds at the time of fledging. There were no significant differences between hatch‐year birds and adults in these measures, indicating that rapid, full maturation occurs early in the post‐fledging period. In combination with previous studies, these data highlight the importance of sampling fledglings to assess full immune ontogeny and suggest that fledgling birds may be more vulnerable to infection than adults.     

Paradoxical surge of corticotropin after glucocorticoid replacement in central adrenal insufficiency

A 78-yr-old man was admitted in emergency with fatigue, anorexia, vomiting, hypothermia (35.1 °C on a hot August day), hypotension (89/56 mmHg) and hyponatraemia (126 mEq/l). Plasma corticotropin and cortisol were severely depressed: 0.84 pmol/L and 33.1 nmol/L respectively (reference range, 1.5-13.9 pmol/L and 110-505 nmol/L, respectively). Thyroid stimulating hormone was low-normal and free-triiodothyronine and free-thyroxine were subnormal. Magnetic resonance imaging revealed swelling of the pituitary gland and the stalk. The patient recovered after glucocorticoid replacement (200 mg/day intravenous hydrocortisone on Day 1 followed by tapering). Central diabetes insipidus which had become apparent had been treated with 1-desamino-8-D-arginine vasopressin. A surge of corticotropin and cortisol, 19.4 pmol/L and 712.1 nmol/L respectively, was found on Day 5 when luteinizing hormone, follicle stimulating hormone, and testosterone were subnormal and prolactin was slightly elevated. Subsequently, corticotropin and cortisol levels normalized together with normalization of luteinizing hormone, follicle stimulating hormone, anti-diuretic hormone, thyroid stimulating hormone, prolactin, testosterone and thyroid hormone levels. Shrinkage of the pituitary gland occurred after one month. Serum immunoglobulin G4 was elevated (3.21 and 6.02 g/l at 1- and 3-month follow-ups respectively). In conclusion, a paradoxical surge of corticotropin after glucocorticoid replacement was observed in a patient with central adrenal insufficiency due to immunoglobulin G4-related hypophysitis. Surge of ACTH in central adrenal insufficiency after glucocorticoid replacement has rarely been reported, and this is the second such case report.     

Identification of a strong binding site for kinesin on the microtubule using mutant analysis of tubulin

The kinesin-binding site on the microtubule has not been identified because of the technical difficulties involved in the mutant analyses of tubulin. Exploiting the budding yeast expression system, we succeeded in replacing the negatively charged residues in the alpha-helix 12 of beta-tubulin with alanine and analyzed their effect on kinesin-microtubule interaction in vitro. The microtubule gliding assay showed that the affinity of the microtubules for kinesin was significantly reduced in E410A, D417A, and E421A, but not in E412A mutant. The unbinding force measurement revealed that in the former three mutants, the kinesin-microtubule interaction in the adenosine 5'-[beta,gamma-imido]triphosphate state (AMP-PNP state) became less stable when a load was imposed towards the microtubule minus end. In parallel with this decreased stability, the stall force of kinesin was reduced. Our results implicate residues E410, D417, and E421 as crucial for the kinesin-microtubule interaction in the strong binding state, thereby governing the size of kinesin stall force.     

Lifespan of Commodities,Part I

Lifespan is an essential parameter for the accounting and analysis of material stocks and flows, one of the main research topics in industrial ecology. Lifespan is also important as a parameter that portrays the current and historical situation of industrial metabolism, which is an area of interest to industrial ecologists. In the present article, the available information from various reports on product lifespan was reviewed. Although we found a large number of data for many durables, the definition of lifespan in published articles varied, which limited our ability to compare reported values. We therefore first defined lifespan and then compared the international and historical data. We compiled more than 1,300 data sets from various sources and identified some differences among the types of goods and among regions. With the reviewed data noted in this article, we established a database, named LiVES (Lifespan Database for Vehicles, Equipment, and Structures), and will disclose it on the Internet to share the information.     

Lifespan of Commodities,Part II

Lifespan of commodities is essential information for material flow analysis and material stock accounting. Lifespan data is available in the literature; however, it varies in definition and in methodology employed. This article reviews and categorizes different types of lifespan distribution and distribution estimation methodologies, and investigates the relationship and differences between lifespan definitions and estimation methodologies. Lifespan distribution of commodities can be classified into five types from two perspectives: base year for which the distribution is drawn, and vertical axis of the distribution. The methodologies for estimating lifespan distribution were classified into four types and the details of each methodology and the relationship to the definition of lifespan were also clarified. This article also examines differences in actual lifespan data—between the types of distribution, the definitions, and the employed methodologies—by comparing reported data in literature. Any of the four methodologies are theoretically applicable and provide the same value of a lifespan; however unless accurate data such as census statistics are available, lifespan data can vary, and therefore we must be very cautious about the representativeness of sample data.     

Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae

Kitasatospora setae NBRC 14216^T (=KM-6054^T) is known to produce setamycin (bafilomycin B1) possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the genus Streptomyces, although they are distinguishable from each other on the basis of cell wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of K. setae NBRC 14216^T as the first Streptomycetaceae genome other than Streptomyces. The genome is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp, predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes. Although these features resemble those of Streptomyces, genome-wide comparison of orthologous genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the Streptomyces genus. Although many of the genes related to morphological differentiation identified in Streptomyces were highly conserved in K. setae, there were some differences such as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the copy number and variation of paralogous components involved in cell wall synthesis.     

Molecular Evolutionary Analysis of the Influenza A(H1N1)pdm,May–September, 2009: Temporal and Spatial Spreading Profile of the Viruses in Japan

Background

In March 2009, pandemic influenza A(H1N1) (A(H1N1)pdm) emerged in Mexico and the United States. In Japan, since the first outbreak of A(H1N1)pdm in Osaka and Hyogo Prefectures occurred in the middle of May 2009, the virus had spread over 16 of 47 prefectures as of June 4, 2009.

Methods/Principal Findings

We analyzed all-segment concatenated genome sequences of 75 isolates of A(H1N1)pdm viruses in Japan, and compared them with 163 full-genome sequences in the world. Two analyzing methods, distance-based and Bayesian coalescent MCMC inferences were adopted to elucidate an evolutionary relationship of the viruses in the world and Japan. Regardless of the method, the viruses in the world were classified into four distinct clusters with a few exceptions. Cluster 1 was originated earlier than cluster 2, while cluster 2 was more widely spread around the world. The other two clusters (clusters 1.2 and 1.3) were suggested to be distinct reassortants with different types of segment assortments. The viruses in Japan seemed to be a multiple origin, which were derived from approximately 28 transported cases. Twelve cases were associated with monophyletic groups consisting of Japanese viruses, which were referred to as micro-clade. While most of the micro-clades belonged to the cluster 2, the clade of the first cases of infection in Japan originated from cluster 1.2. Micro-clades of Osaka/Kobe and the Fukuoka cases, both of which were school-wide outbreaks, were eradicated. Time of most recent common ancestor (tMRCA) for each micro-clade demonstrated that some distinct viruses were transmitted in Japan between late May and early June, 2009, and appeared to spread nation-wide throughout summer.

Conclusions

Our results suggest that many viruses were transmitted from abroad in late May 2009 irrespective of preventive actions against the pandemic influenza, and that the influenza A(H1N1)pdm had become a pandemic stage in June 2009 in Japan.